A Novel Algorithm for Enhanced Structural Motif Matching in Proteins

J Comput Biol. 2015 Jul;22(7):698-713. doi: 10.1089/cmb.2014.0263. Epub 2015 Feb 19.


As widely discussed in literature, spatial patterns of amino acids, so-called structural motifs, play an important role in protein function. The functionally responsible part of proteins often lies in an evolutionarily highly conserved spatial arrangement of only a few amino acids, which are held in place tightly by the rest of the structure. Those recurring amino acid arrangements can be seen as patterns in the three-dimensional space and are known as structural motifs. In general, these motifs can mediate various functional interactions, such as DNA/RNA targeting and binding, ligand interactions, substrate catalysis, and stabilization of the protein structure. Hence, characterizing and identifying such conserved structural motifs can contribute to the understanding of structure-function relationships. Therefore, and because of the rapidly increasing number of solved protein structures, it is highly desirable to identify, understand, and moreover to search for structurally scattered amino acid motifs. This work aims at the development and the implementation of a novel and robust matching algorithm to detect structural motifs in large sets of target structures. The proposed methods were combined and implemented to a feature-rich and easy-to-use command line software tool written in Java.

Keywords: algorithms; computational molecular biology; protein motifs; protein structure.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Motifs
  • Catalytic Domain
  • Hydrolases / chemistry
  • Models, Molecular*
  • Phosphopyruvate Hydratase / chemistry
  • Protein Structure, Secondary
  • Software*


  • Hydrolases
  • haloacetate dehalogenase
  • Phosphopyruvate Hydratase